PEtab

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Proposal: Different languages for model specification

2

# Motivation There are a number of formats for specifying models in systems biology, each with their specific strengths and weaknesses. PEtab version 1.0.0 only allows Systems Biology Markup Language...

dweindl

Time-dependent changes in component values

6

related: #16 #540 If you are already familiar with this, you could skip straight to the "Feedback" section and share your thoughts. A couple of (currently unofficial) PEtab extensions have...

dilpath

Allow species in `yValues` of the visualization table

2

**Which problem would you like to address? Please describe.** Atm it seems like [only observables can be plotted on the y axis](https://petab.readthedocs.io/en/stable/documentation_data_format.html#id4). It would be nice to also be able...

paulflang

PEtab extension for NLME

20

**Which problem would you like to address? Please describe.** Currently, PEtab does not allow to express nonlinear mixed effects models (i.e containing fixed (population) and random (patient-specific) effects). These models...

paulflang

Update PETab to be model format agnostic

4

**Which problem would you like to address? Please describe.** The CellML team is about to implement support for parameter estimation in OpenCor, and originally investigated PETab as the format to...

luciansmith

Allow using observable IDs in `observableFormula` and `noiseFormula`

1

Following up on #543 and the discussion during the last PEtab editor meeting: There was general consent to allow using observableIDs in the `noiseFormula` column in the observables table. What...

dweindl

Nowhere close to final. **Do not merge.**

dweindl

Allow using observables in noiseFormula

2

Currently it is not allowed to use observable IDs in `noiseFormula` in the observables table (#368). It would be great to allow that. This would convenient for specifying relative errors....

dweindl

Clarification/specification of order of condition changes required

5

Depending on the order of the changes applied for a condition the model will be in a different state. I.e. the order of the columns matters in the condition table....

matthiaskoenig

No Noise

13

Hi, we would like to perform parameter estimation for an ODE-model without considering any stochastic effects. Is it possible to define a PETAB problem without a noise parameter/set the noise...

tinop99